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Imported Upstream version 0.2.0
[tabix.git]
/
tabix.1
diff --git
a/tabix.1
b/tabix.1
index 4b5eea25057be28b6a7fa749ef2272a14ebfb313..3b82c766d8059d3f41adf66e2e2b95a040d7b3ef 100644
(file)
--- a/
tabix.1
+++ b/
tabix.1
@@
-1,4
+1,4
@@
-.TH tabix 1 "1
6 March 2009" "tabix-0.1.1
" "Bioinformatics tools"
+.TH tabix 1 "1
1 May 2010" "tabix-0.2.0
" "Bioinformatics tools"
.SH NAME
.PP
bgzip - Block compression/decompression utility
.SH NAME
.PP
bgzip - Block compression/decompression utility
@@
-15,7
+15,7
@@
tabix - Generic indexer for TAB-delimited genome position files
.RI [ file ]
.PP
.B tabix
.RI [ file ]
.PP
.B tabix
-.RB [ \-0 ]
+.RB [ \-0
lf
]
.RB [ \-p
.R gff|bed|sam|vcf]
.RB [ \-s
.RB [ \-p
.R gff|bed|sam|vcf]
.RB [ \-s
@@
-69,8
+69,8
@@
are all stored in the index file and thus not used in data retrieval. [1]
Column of start chromosomal position. [4]
.TP
.BI "-e " INT
Column of start chromosomal position. [4]
.TP
.BI "-e " INT
-Column of end chromosomal position. The end column can be the same as
-start column
,
[5]
+Column of end chromosomal position. The end column can be the same as
the
+start column
.
[5]
.TP
.BI "-S " INT
Skip first INT lines in the data file. [0]
.TP
.BI "-S " INT
Skip first INT lines in the data file. [0]
@@
-81,10
+81,16
@@
Skip lines started with character CHAR. [#]
.B -0
Specify that the position in the data file is 0-based (e.g. UCSC files)
rather than 1-based.
.B -0
Specify that the position in the data file is 0-based (e.g. UCSC files)
rather than 1-based.
+.TP
+.B -f
+Force to overwrite the index file if it is present.
+.TP
+.B -l
+List the sequence names stored in the index file.
.RE
.SH EXAMPLE
.RE
.SH EXAMPLE
-
grep -v ^"#" unsorted.gff | sort -k1,1 -k4,4n | bgzip -c
> sorted.gff.gz;
+
(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip
> sorted.gff.gz;
tabix -p gff sorted.gff.gz;
tabix -p gff sorted.gff.gz;